Why are the other boys unable to understand Simon in "Lord of the Flies"?
To answer this question you need to think about the character of Simon, what he represents, and how he compares with the other characters in the novel.
If you consider that Ralph and Jack represent, respectively, civilisation and savagery, Simon exists on a completely different plane. He can be said to represent a mystical, almost spiritual goodness that has a deep connection with nature. It is clear that looking at one of the major themes of the novel - the savagery of mankind - that the boys abandon morality not necessarily because they are innately immoral, but they are free from the constrictions of adults that prevent them from behaving in an immoral way. That is to say that we are conditioned to act in a moral way rather than being innately moral. All the boys participate in the hunt-dance, for example, even Ralph and Piggy.
Unlike everyone else on the island Simon acts morally, not out of guilt or shame, but because he believes in the innate value of morality itself. Because of his different standpoint and perspective, he is the first to realise the truth about the Beast - that it represents the savagery lurking inside the boys. But again, because of his different position in the novel, the other boys do not understand this and kill him before he can properly explain.